GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns

Angles, Renzo; Arenas-Salinas, Mauricio; García, Roberto; Reyes-Suarez, Jose Antonio; Pohl, Ehmke

doi:10.1186/s12859-020-3352-x

GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns

Angles, Renzo; Arenas-Salinas, Mauricio; García, Roberto; Reyes-Suarez, Jose Antonio; Pohl, Ehmke

Authors

Renzo Angles

Mauricio Arenas-Salinas

Roberto García

Jose Antonio Reyes-Suarez

Professor Ehmke Pohl ehmke.pohl@durham.ac.uk
Interim Director

Abstract

Background: In the field of protein engineering and biotechnology, the discovery and characterization of structural patterns is highly relevant as these patterns can give fundamental insights into protein-ligand interaction and protein function. This paper presents GSP4PDB, a bioinformatics web tool that enables the user to visualize, search and explore protein-ligand structural patterns within the entire Protein Data Bank. Results: We introduce the notion of graph-based structural pattern (GSP) as an abstract model for representing protein-ligand interactions. A GSP is a graph where the nodes represent entities of the protein-ligand complex (amino acids and ligands) and the edges represent structural relationships (e.g. distances ligand - amino acid). The novel feature of GSP4PDB is a simple and intuitive graphical interface where the user can “draw” a GSP and execute its search in a relational database containing the structural data of each PDB entry. The results of the search are displayed using the same graph-based representation of the pattern. The user can further explore and analyse the results using a wide range of filters, or download their related information for external post-processing and analysis. Conclusions: GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.

Citation

Angles, R., Arenas-Salinas, M., García, R., Reyes-Suarez, J. A., & Pohl, E. (2020). GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns. BMC Bioinformatics, 21(S2), Article 85. https://doi.org/10.1186/s12859-020-3352-x

Journal Article Type	Article
Online Publication Date	Mar 11, 2020
Publication Date	2020
Deposit Date	Apr 1, 2020
Publicly Available Date	Apr 2, 2020
Journal	BMC Bioinformatics
Electronic ISSN	1471-2105
Publisher	BioMed Central
Peer Reviewed	Peer Reviewed
Volume	21
Issue	S2
Article Number	85
DOI	https://doi.org/10.1186/s12859-020-3352-x
Public URL	https://durham-repository.worktribe.com/output/1274205

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